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Update to topic porechop/* #12610

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51cc789
Update to topic
LouisLeNezet Aug 6, 2026
63179d1
Merge branch 'master' into porechop
LouisLeNezet Aug 7, 2026
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13 changes: 2 additions & 11 deletions modules/nf-core/porechop/abi/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,8 @@ process PORECHOP_ABI {

output:
tuple val(meta), path("*.fastq.gz"), emit: reads
tuple val(meta), path("*.log"), emit: log
path "versions.yml", emit: versions
tuple val(meta), path("*.log") , emit: log
tuple val("${task.process}"), val('porechop_abi'), eval("porechop_abi --version"), topic: versions, emit: versions_porechop_abi

when:
task.ext.when == null || task.ext.when
Expand All @@ -34,21 +34,12 @@ process PORECHOP_ABI {
${args} \\
--output ${prefix}.fastq.gz \\
| tee ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
porechop_abi: \$( porechop_abi --version )
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}.porechop_abi"
"""
echo "" | gzip > ${prefix}.fastq.gz
touch ${prefix}.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
porechop_abi: \$( porechop_abi --version )
END_VERSIONS
"""
}
37 changes: 26 additions & 11 deletions modules/nf-core/porechop/abi/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,19 +1,18 @@
name: "porechop_abi"
description: Extension of Porechop whose purpose is to process adapter sequences in
ONT reads.
description: Extension of Porechop whose purpose is to process adapter sequences in ONT reads.
keywords:
- porechop_abi
- adapter
- nanopore
tools:
- "porechop_abi":
description: Extension of Porechop whose purpose is to process adapter sequences
in ONT reads.
description: Extension of Porechop whose purpose is to process adapter sequences in ONT reads.
homepage: "https://github.com/bonsai-team/Porechop_ABI"
documentation: "https://github.com/bonsai-team/Porechop_ABI"
tool_dev_url: "https://github.com/bonsai-team/Porechop_ABI"
doi: "10.1101/2022.07.07.499093"
licence: ["MIT"]
licence:
- "MIT"
identifier: ""
input:
- - meta:
Expand Down Expand Up @@ -56,13 +55,29 @@ output:
description: Log file containing stdout information
pattern: "*.log"
ontologies: []
versions_porechop_abi:
- - ${task.process}:
type: string
description: The name of the process
- porechop_abi:
type: string
description: The name of the tool
- porechop_abi --version:
type: eval
description: The expression to obtain the version of the tool

topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The name of the process
- porechop_abi:
type: string
description: The name of the tool
- porechop_abi --version:
type: eval
description: The expression to obtain the version of the tool

authors:
- "@sofstam"
- "LilyAnderssonLee"
Expand Down
18 changes: 6 additions & 12 deletions modules/nf-core/porechop/abi/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,47 +14,41 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test'], // meta map
[ id:'test'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
]
input[1] = []
input[1] = []
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.reads,
file(process.out.log.get(0).get(1)).readLines()[20..40],
process.out.versions).match()
}
{ assert snapshot(sanitizeOutput(process.out, unstableKeys:["log"])).match() }
)
}
}

test("sarscov2-nanopore - stub") {

options "-stub"

when {

process {
"""
input[0] = [
[ id:'test'], // meta map
[ id:'test'],
file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
]
input[1] = []
input[1] = []
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
88 changes: 32 additions & 56 deletions modules/nf-core/porechop/abi/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,69 +1,41 @@
{
"sarscov2-nanopore": {
"content": [
[
[
{
"id": "test"
},
"test.porechop_abi.fastq.gz:md5,886fdb859fb50e0dddd35007bcff043e"
]
],
[
" Best \u001b[0m",
" read Best \u001b[0m",
" start read end\u001b[0m",
" \u001b[4mSet %ID %ID \u001b[0m",
" \u001b[32mSQK-NSK007 100.0 73.1\u001b[0m",
" Rapid 40.4 0.0",
" RBK004_upstream 77.5 0.0",
" SQK-MAP006 75.8 72.7",
" SQK-MAP006 short 65.5 66.7",
" PCR adapters 1 73.9 69.6",
" PCR adapters 2 80.0 72.7",
" PCR adapters 3 70.8 69.6",
" 1D^2 part 1 71.4 70.0",
" 1D^2 part 2 84.8 75.8",
" cDNA SSP 63.0 61.7",
" \u001b[32mBarcode 1 (reverse) 100.0 100.0\u001b[0m",
" Barcode 2 (reverse) 70.8 69.2",
" Barcode 3 (reverse) 76.0 70.4",
" Barcode 4 (reverse) 74.1 71.4",
" Barcode 5 (reverse) 77.8 80.8",
" Barcode 6 (reverse) 73.1 70.8"
],
[
"versions.yml:md5,0e9e5e0d35a68ff8e6490c949b257f98"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-10T10:27:24.536642628"
},
"sarscov2-nanopore - stub": {
"content": [
{
"0": [
"log": [
[
{
"id": "test"
},
"test.porechop_abi.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
"test.porechop_abi.log"
]
],
"1": [
"reads": [
[
{
"id": "test"
},
"test.porechop_abi.log:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.porechop_abi.fastq.gz:md5,886fdb859fb50e0dddd35007bcff043e"
]
],
"2": [
"versions.yml:md5,0e9e5e0d35a68ff8e6490c949b257f98"
],
"versions_porechop_abi": [
[
"PORECHOP_ABI",
"porechop_abi",
"0.5.0"
]
]
}
],
"timestamp": "2026-08-06T17:59:25.403246301",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
},
"sarscov2-nanopore - stub": {
"content": [
{
"log": [
[
{
Expand All @@ -80,15 +52,19 @@
"test.porechop_abi.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,0e9e5e0d35a68ff8e6490c949b257f98"
"versions_porechop_abi": [
[
"PORECHOP_ABI",
"porechop_abi",
"0.5.0"
]
]
}
],
"timestamp": "2026-08-06T17:59:32.504538143",
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-10T10:27:30.502715737"
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
}
}
17 changes: 4 additions & 13 deletions modules/nf-core/porechop/porechop/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -7,14 +7,13 @@ process PORECHOP_PORECHOP {
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2b/2bce1f10c51906a66c4c4d3a7485394f67e304177192ad1cce6cf586a3a18bae/data' :
'community.wave.seqera.io/library/porechop_pigz:d1655e5b5bad786c' }"


input:
tuple val(meta), path(reads)

output:
tuple val(meta), path("*.fastq.gz"), emit: reads
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('porechop'), eval("porechop --version"), topic: versions, emit: versions_porechop

when:
task.ext.when == null || task.ext.when
Expand All @@ -24,15 +23,11 @@ process PORECHOP_PORECHOP {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
porechop \\
-i $reads \\
-t $task.cpus \\
$args \\
-i ${reads} \\
-t ${task.cpus} \\
${args} \\
-o ${prefix}.fastq.gz \\
> ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
porechop: \$( porechop --version )
END_VERSIONS
"""

stub:
Expand All @@ -41,9 +36,5 @@ process PORECHOP_PORECHOP {
touch ${prefix}.fastq
gzip ${prefix}.fastq
touch ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
porechop: \$( porechop --version )
END_VERSIONS
"""
}
31 changes: 24 additions & 7 deletions modules/nf-core/porechop/porechop/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,8 @@ tools:
documentation: "https://github.com/rrwick/Porechop"
tool_dev_url: "https://github.com/rrwick/Porechop"
doi: "10.1099/mgen.0.000132"
licence: ["GPL v3"]
licence:
- "GPL v3"
identifier: ""
input:
- - meta:
Expand Down Expand Up @@ -48,13 +49,29 @@ output:
description: Log file containing stdout information
pattern: "*.log"
ontologies: []
versions_porechop:
- - ${task.process}:
type: string
description: The name of the process
- porechop:
type: string
description: The name of the tool
- porechop --version:
type: eval
description: The expression to obtain the version of the tool

topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The name of the process
- porechop:
type: string
description: The name of the tool
- porechop --version:
type: eval
description: The expression to obtain the version of the tool

authors:
- "@ggabernet"
- "@jasmezz"
Expand Down
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